My syntax was just a bit off... RELDEF :: include CUI
My examples in the previous note did not have 'include'. You can see some more info on usage here : https://metacpan.org/pod/UMLS::Similarity::lesk#TYPICAL-USAGE-EXAMPLES In general definition coverage of SNOMEDCT is not great, so I'm not surprised by all the zero scores. If you have your own dictionary you can provide that via the --dict option, and/or you may want to consider other sources that have more definitions. More soon, Ted On Tue, Jul 29, 2014 at 4:41 PM, Ted Pedersen <tpede...@d.umn.edu> wrote: > I'll post a more detailed answer in the next day or two, but at least > briefly, when you use RELDEF you are specifying the CUI from which a > definition is taken. > > So, in the case of > > RELDEF :: CUI > > you are simply saying give me the definition of the CUIs I have specified > in similarity.pl. This is the natural case. > > You can also say things like > > RELDEF :: CUI,PAR > > which means give me the definitions of the CUIs I have specified, plus > those associated with the parents of those CUIs. this is how we created an > extended gloss overlaps (where the definition of a CUI includes the > definition of the CUI itself plus the definitions of its parents). > > RELDEF :: TERM means that rather than using a definition, you use the > associated terms of the given CUIs in place of a definition. > > So, that's a start of a response, I'll continue with more in the next day > or two. > > Cordially, > Ted > > > On Mon, Jul 28, 2014 at 6:02 PM, chaitanyapshiv...@yahoo.co.in > [umls-similarity] <umls-similarity@yahoogroups.com> wrote: > >> >> >> Hi >> >> >> The Lesk algorithm computes similarity between glosses of two concepts. >> As per the article (Banerjee and Pedersen 2002) an overlap is computed as >> the longest sequence of one or more consecutive words. >> >> >> I ran lesk (UMLS3013AA) on a set of 58K pairs using >> >> >> config1 >> >> SABDEF:: SNOMEDCT >> >> RELDEF:: CUI >> >> and almost all pairs had a score of -1. >> >> >> But with >> >> config2 >> >> SABDEF:: SNOMEDCT >> >> RELDEF:: TERM >> >> has a number of positive scores. >> >> >> I would like to know >> >> 1. What exactly is the gloss when RELDEF has TERM ? Is it the str column >> in the mrconso table of that cui ? >> >> >> 2. As per my understanding of the documentation, CUI in RELDEF implies >> that the cui definition is fetched from the mrdef table, which is treated >> as a gloss. Is this correct ? If CUI is not specified, what is the gloss ? >> In either case i am unable to understand why config1 gets no output. >> >> The concepts i am working on have been extracted from a dataset >> associated with the same disease. I ran similarity measures on them many >> yield positive output for similarity. >> >> >> 3. The published paper is for WordNet and the configurations are specific >> to UMLS. It would be great if you can provide brief commentary on what >> constitutes a gloss for different options in UMLS. >> >> >> Thanks, >> >> Chaitanya. >> >> >> >> >> >> > > > > -- > Ted Pedersen > http://www.d.umn.edu/~tpederse > -- Ted Pedersen http://www.d.umn.edu/~tpederse
